Load and tidy data sets

Risk Factor Analysis

## Start:  AIC=572.55
## isolate ~ year + school + school_year + sex + shares_drinks
## 
##                 Df Deviance    AIC
## - school_year    3   557.93 567.93
## - shares_drinks  1   557.53 571.53
## - school         1   558.52 572.52
## <none>               556.55 572.55
## - year           1   564.05 578.05
## - sex            1   568.13 582.13
## 
## Step:  AIC=567.93
## isolate ~ year + school + sex + shares_drinks
## 
##                 Df Deviance    AIC
## - shares_drinks  1   559.75 567.75
## <none>               557.93 567.93
## - school         1   563.05 571.05
## + school_year    3   556.55 572.55
## - sex            1   569.32 577.32
## - year           1   574.20 582.20
## 
## Step:  AIC=567.75
## isolate ~ year + school + sex
## 
##                 Df Deviance    AIC
## <none>               559.75 567.75
## + shares_drinks  1   557.93 567.93
## + school_year    3   557.53 571.53
## - school         1   565.73 571.73
## - sex            1   573.71 579.71
## - year           1   576.18 582.18
Characteristic OR1 95% CI1 p-value
year
    1 — —
    2 2.26 1.52, 3.37 <0.001
school
    1 — —
    2 0.50 0.28, 0.87 0.016
sex
    F — —
    M 2.12 1.43, 3.16 <0.001
1 OR = Odds Ratio, CI = Confidence Interval 
##  Tjur's R2 
## 0.08741338

Network Plots

Strain Type

School Year

Gender segregation

Sharing Drinks

Single School, Comparisons (Main Manuscript)

Network statistics

## # A tibble: 4 × 5
## # Groups:   school [2]
##   school  year edges nodes participants
##    <int> <int> <int> <int>        <int>
## 1      1     1  1330   562          183
## 2      1     2  1263   507          185
## 3      2     1   355   225           45
## 4      2     2   200   145           20

Characteristic School 1, Year 1 School 1, Year 2 School 2, Year 1 School 2, Year 2
Median (95% CI) Median (95% CI) Median (95% CI) Median (95% CI)
Clustering Coefficient 0.412 (0.394, 0.429) 0.425 (0.401, 0.445) 0.494 (0.453, 0.509) 0.4091 (0.4091, 0.4091)
Reciprocity 0.468 (0.435, 0.502) 0.445 (0.410, 0.478) 0.43 (0.37, 0.50) 0.55 (0.45, 0.64)
Mean Distance 6.93 (6.10, 7.65) 8.05 (7.04, 9.31) 3.23 (2.80, 3.45) 2.0200 (2.0200, 2.0200)
No. of Communities 37.0 (30.0, 43.0) 29.00 (24.00, 35.00) 13.00 (11.00, 15.00) 12.00 (9.00, 13.00)
Community Size 61.4 (51.5, 74.1) 61.1 (53.8, 69.9) 18.38 (16.73, 21.07) 7.50 (7.50, 8.60)
Characteristic Year 1 (95% CI) Year 2 (95% CI)
Assortativity (Year) 0.92 (0.89, 0.94) 0.80 (0.76, 0.84)
Assortativity (Gender) 0.61 (0.57, 0.66) 0.77 (0.73, 0.80)
Assortativity (Shares Drinks) 0.27 (0.21, 0.32) 0.22 (0.17, 0.27)
Assortativity (Shares Drinks M) 0.01 (-0.09, 0.10) 0.01 (-0.07, 0.10)
Assortativity (Shares Drinks F) 0.33 (0.26, 0.40) 0.34 (0.27, 0.42)
Assortativity (Swab 1) 0.00 (-0.05, 0.06) 0.05 (0.00, 0.11)
Assortativity (Swab 2) 0.00 (-0.05, 0.06) 0.05 (-0.01, 0.10)
 
## starts_with("assortativity") ~ "continuous"